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TreeDyn: towards dynamic graphics and annotations for analyses of trees

François Chevenet, Christine Brun, Anne-Laure Bañuls, Bernard Jacq, Richard Christen
2006 BMC Bioinformatics  
Results: We have developed TreeDyn, a tool using annotations and dynamic graphical methods for editing and analyzing multiple trees.  ...  Conclusion: TreeDyn is a tree visualization and annotation tool which includes tools for tree manipulation and annotation and uses meta-information through dynamic graphical operators or scripting to help  ...  Thanks are due to Sylvain Godreuil, Camille Szmaragd, Amélie Véron, David Zolli, Alain Guénoche, Miguel Lopez Ferber for data and testing the software and to Philip Agnew for carefully reading the manuscript  ... 
doi:10.1186/1471-2105-7-439 pmid:17032440 pmcid:PMC1615880 fatcat:zdcjpuoamzazng5iqjpk4wa63e

Page 1414 of Genetics Vol. 177, Issue 3 [page]

2007 Genetics  
CHRISTEN, 2006 TreeDyn: towards dynamic graphics and annotations for analyses of trees. BMC Bioinformatics 7: 439. Cuys, S., A. DAHANUKAR, A. WICKENS and J. R.  ...  Robertson for consulta- tion on the simulans and yakuba annotations.  ... 

Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future

Georgios A. Pavlopoulos, Dimitris Malliarakis, Nikolas Papanikolaou, Theodosis Theodosiou, Anton J. Enright, Ioannis Iliopoulos
2015 GigaScience  
We focus on the latest libraries and programming languages that enable more effective, efficient and faster approaches for visualizing biological concepts, and also comment on the future human-computer  ...  interaction trends that would enable for enhancing visualization further.  ...  variables/values pairs of annotations, independently of the tree topologies http://www.treedyn.org/ TreeGraph [295] A graphical editor for phylogenetic trees that allows many graphical formats  ... 
doi:10.1186/s13742-015-0077-2 pmid:26309733 pmcid:PMC4548842 fatcat:w7hxgunagfcbxctnio7kwnucsy

Genotyping Staphylococcus aureus Isolates with RS-PCR from Chicken Meat in Chennai City

S. J. Deepak, K. Porteen, A. Elango, T. M. A. Senthil Kumar, R. Narendra Babu, S. Sureshkannan, S. Wilfred Ruban
2019 International Journal of Current Microbiology and Applied Sciences  
TreeDyn: towards dynamic graphics and annotations for analyses of trees. BMC Bioinformatics. 7: 439.  ...  The dendograms were obtained to assess the genetic relationship among the S. aureus isolates with RS-PCR were and visualized using the online Phylogenetic tree (newick) viewer by TreeDyn by Phylogeny.fr  ... 
doi:10.20546/ijcmas.2019.812.294 fatcat:pt7nfosu7ng5rc3gn5bj5nwpme

A reference guide for tree analysis and visualization

Georgios A Pavlopoulos, Theodoros G Soldatos, Adriano Barbosa-Silva, Reinhard Schneider
2010 BioData Mining  
Sequencing technologies become cheaper and easier to use and, thus, large-scale evolutionary studies towards the origins of life for all species and their evolution becomes more and more challenging.  ...  In this study, we review tools that are currently available for the visualization of biological trees and analysis, mainly developed during the last decade.  ...  Tree Editing TaxonTree [75] , TreeEdit [76] , TreeDyn [77] , BAOBAB [46] , MacClade [57] , Mavric [78] , TreeGraph [45] Tree Annotation TaxonTree [75] , TreeEdit [76] , TreeDyn [77] , BAOBAB  ... 
doi:10.1186/1756-0381-3-1 pmid:20175922 pmcid:PMC2844399 fatcat:k2k6u72nandljivhdbxvstuy2u

Both clinical and environmental Caulobacter species act as opportunistic pathogens [article]

Gabriel M Moore, Zemer Gitai
2019 bioRxiv   pre-print
Given the proposed environmental and medical applications for C. crescentus, understanding the potential pathogenicity and human health implications of this bacterium is crucial.  ...  Taken together, our findings redefine Caulobacters as opportunistic pathogens and highlight the importance of broadening our methods for identifying and characterizing pathogens.  ...  TreeDyn: towards dynamic graphics and 466 annotations for analyses of trees.  ... 
doi:10.1101/645515 fatcat:j5yjzjixxjdwlfwntsqwlahnlq

Sequence analysis of two alleles reveals that intra-and intergenic recombination played a role in the evolution of the radish fertility restorer (Rfo)

José R Hernandez Mora, Eric Rivals, Hakim Mireau, Françoise Budar
2010 BMC Plant Biology  
Our analyses strongly suggest that present coding sequences of Rfo PPR genes result from intragenic recombination.  ...  The Rfo locus and PPR genes therein are likely to evolve as a result of intergenic and intragenic recombination. It is therefore not possible to determine  ...  Jacq, and R. Christen: TreeDyn: towards dynamic graphics and annotations for analyses of trees BMC Bioinformatics 2006, 7: 439. ). 55. Dellaporta, J., J. Wood, and J.  ... 
doi:10.1186/1471-2229-10-35 pmid:20178653 pmcid:PMC2848758 fatcat:3t7zleehjffdhjde4vna4fzevu

Genetic Diversity and Population Structure of Mycobacterium marinum: New Insights into Host and Environmental Specificities

V. Broutin, A.-L. Banuls, A. Aubry, N. Keck, M. Choisy, J.-F. Bernardet, C. Michel, J.-C. Raymond, C. Libert, A. Barnaud, P. Stragier, F. Portaels (+8 others)
2012 Journal of Clinical Microbiology  
Jacq, and R. Christen. 2006. TreeDyn: 395 towards dynamic graphics and annotations for analyses of trees. BMC Bioinformatics 396 7:439. 397 8. dos Santos, N. M., A. do Vale, M. J. Sousa, and M. T.  ...  PAUP 4.0 (27) was used for tree 150 elaboration and Treedyn (7) for tree visualization and annotation. 151 Statistical analysis.  ... 
doi:10.1128/jcm.01274-12 pmid:22952269 pmcid:PMC3486196 fatcat:ftuncbmk7fauzfm7x3nzqqmga4

Integrated whole-genome sequencing and temporospatial analysis of a continuing Group A Streptococcus epidemic

Nahuel Fittipaldi, Gregory J Tyrrell, Donald E Low, Irene Martin, David Lin, Kumar L Hari, James M Musser
2013 Emerging Microbes and Infections  
TreeDyn: towards dynamic We thank the following hospitals or provincial public health laboratories for graphics and annotations for analyses of trees.  ...  were created using Bioinformatic analysis SplitsTree28 and graphically edited with TreeDyn.29 The Neighbor-join  ... 
doi:10.1038/emi.2013.13 pmid:26038455 pmcid:PMC3630956 fatcat:pd3mebnx3jgw7jysqayub7xuwm

Re-evaluating inheritance in genome evolution: widespread transfer of LINEs between species [article]

Atma Ivancevic, Daniel Kortschak, Terry Bertozzi, David Adelson
2017 bioRxiv   pre-print
With the advancement of genome sequencing technologies and bioinformatics tools, we anticipate our study to be the first of many large-scale phylogenomic analyses exploring the role of HT in genome evolution  ...  Given that these TEs make up nearly half of the genome sequence in today's mammals, our results provide the first evidence that HT can have drastic and long-term effects on the new host genomes.  ...  a much-needed sanity check and Matt Westlake for HPC support above and beyond the call of duty.  ... 
doi:10.1101/106914 fatcat:ich6cfgosrdyfenj44jewiigaq

Diversity of Beetle Genes Encoding Novel Plant Cell Wall Degrading Enzymes

Yannick Pauchet, Paul Wilkinson, Ritika Chauhan, Richard H. ffrench-Constant, Sue Cotterill
2010 PLoS ONE  
Given the huge diversity of beetles alive today, and the diversity of their lifestyles and diets, we predict that beetle guts will emerge as an important new source of enzymes for use in biotechnology.  ...  Plant cell walls are a heterogeneous mixture of polysaccharides and proteins that require a range of different enzymes to degrade them.  ...  Acknowledgments We thank Margaret Hughes at Liverpool for 454 sequencing, Tom Tregenza, Guy Smagghe, Tom Philips and Frédéric Gressent for provision of insects, and two anonymous reviewers for constructive  ... 
doi:10.1371/journal.pone.0015635 pmid:21179425 pmcid:PMC3003705 fatcat:wr6ppjfnv5ebdm6t2adrnfpo4u

Identification of Photorhabdus symbionts by MALDI-TOF MS

Virginia Hill, Peter Kuhnert, Matthias Erb, Ricardo A R Machado
2020 Microbiology  
Our study demonstrates the suitability and limitations of MALDI-TOF-based identification methods for assessment of the taxonomic position and identification of Photorhabdus isolates.  ...  The extended reference database was then used for identification based on the direct transfer sample preparation method and the protein fingerprint of single colonies.  ...  TreeDyn: towards dynamic graphics 384 and annotations for analyses of trees. BMC Bioinformatics 7:357. doi:10.1186/1471-2105-7-439. 385 62. Letunic I, Bork P. 2016.  ... 
doi:10.1099/mic.0.000905 pmid:32301690 fatcat:wjverethunbujm5grzsgy7y5re

Centromere Binding and Evolution of Chromosomal Partition Systems in the Burkholderiales

F. M. Passot, V. Calderon, G. Fichant, D. Lane, F. Pasta
2012 Journal of Bacteriology  
Jacq, and R. Christen. 2006. 506 TreeDyn: towards dynamic graphics and annotations for analyses of trees. Davis, M. A., K. A. Martin, and S. J. Austin. 1990.  ...  Tree topology, branch length and substitution rate 472 parameters were optimised. The tree is rooted using NJplot (46), drawn using Treedyn 473 (11) and coloured according to ParB subfamilies.  ...  Features of par loci of B.cenocepacia J2315 replicons and other model systems In the "Replicon" column, c1, c2, c3 and MP refer to chromosomes 1, 2, 3 and to mega-plasmids respectively; (Ia) and (Ib) refer  ... 
doi:10.1128/jb.00041-12 pmid:22522899 pmcid:PMC3434744 fatcat:6m4mrxxvqfcgdkxdelygk54ple

Phylogeny and expression of canonical transient receptor potential (TRPC) genes in developing zebrafish

Valentin Von Niederhäusern, Edda Kastenhuber, Andreas Stäuble, Matthias Gesemann, Stephan C.F. Neuhauss
2013 Developmental Dynamics  
Molecular cloning of the coding sequences confirmed that all of our annotated sequences are transcribed.  ...  in the nervous system.  Distinct and dynamic expression patterns in various sensory and motor systems can be detected during development.  ...  Graphical representation and edition of the phylogenetic tree were performed with TreeDyn (v198.3) and the svg file imported into CoralDraw (version X5; Coral Corporation Ottawa, Canada) for final  ... 
doi:10.1002/dvdy.24041 pmid:24038627 fatcat:ilnw27hxyvedvhgv2iyygdbolu

Whole genome comparative analysis of transposable elements provides new insight into mechanisms of their inactivation in fungal genomes

Joëlle Amselem, Marc-Henri Lebrun, Hadi Quesneville
2015 BMC Genomics  
Transposable Elements (TEs) are key components that shape the organization and evolution of genomes.  ...  Both mechanisms require specific cytosine DNA Methyltransferases (RID1/Masc1) of the Dnmt1 superfamily. Results: We annotated TE sequences from 10 fungal genomes with different TE content (1-70%).  ...  We would like to gratefully acknowledge Ludovic Mallet for the re-annotation of transposable elements in Magnaporthe oryzae.  ... 
doi:10.1186/s12864-015-1347-1 pmid:25766680 pmcid:PMC4352252 fatcat:2p3iv6wdkfeurovsj2kvwgtzvm
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